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Don't believe there's a limit to e-filing a 2nd 1120X. I'd save a copy of the original 1120X for the records and use the original 1120X to prepare this 2nd 1120X (so that you don't get charged for e-filing a "new" return). The originally reported amounts on this 2nd 1120X should be what's on the original 1120X. So long as the IRS has already processed (which may be some time after acceptance) and does not object to those changes registered on the original 1120X, you shouldn't have any problem with mismatch.